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PMID: 27337980 Published · epublish English Journal Article

The Ensembl gene annotation system.

Database : the journal of biological databases and curation ·Vol. 2016 ·2016-00-00

Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SM

Abstract

The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html.

MeSH Terms
Animals Databases, Nucleic Acid Databases, Protein Humans Internet Mice Molecular Sequence Annotation/methods
Authors & Affiliations
24 authors, click to expand affiliations / ORCID
Aken Bronwen L
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK [email protected] [email protected].
Ayling Sarah
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Present addresses: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK.
Barrell Daniel
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK.
Clarke Laura
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Curwen Valery
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Fairley Susan
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Fernandez Banet Julio
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Pfizer Inc, 10646 Science Center Dr, San Diego, CA 92121, USA.
Billis Konstantinos
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
García Girón Carlos
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Hourlier Thibaut
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Howe Kevin
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Kähäri Andreas
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Institutionen för cell-och molekylärbiologi, Uppsala University, Husargatan 3, Uppsala 752 37, Sweden.
Kokocinski Felix
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Martin Fergal J
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Murphy Daniel N
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Nag Rishi
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Ruffier Magali
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Schuster Michael
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna a-1090, Austria.
Tang Y Amy
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Vogel Jan-Hinnerk
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.
White Simon
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
Zadissa Amonida
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Flicek Paul
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Searle Stephen M J
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK [email protected] [email protected].
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Article Info
Journal
Database : the journal of biological databases and curation
Abbr.
Database (Oxford)
ISSN
1758-0463
DOI
10.1093/database/baw093
Email
[email protected]
[email protected]
Published
2016-00-00
Epub
2016-00-23
Language
English
Region
England
NLM ID
101517697
PMCID
PMC4919035
Subset
IM
Grants
Wellcome Trust · WT095908 · United Kingdom
Wellcome Trust · WT098051 · United Kingdom
NHGRI NIH HHS · U54 HG004555 · United States
NHGRI NIH HHS · U41 HG007234 · United States
NICHD NIH HHS · R01 HD074078 · United States
Biotechnology and Biological Sciences Research Council · BB/M011615/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/I025506/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/I025360/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/I025360/2 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/M011461/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/K009524/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/M018458/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BBS/B/13446 · United Kingdom
Biotechnology and Biological Sciences Research Council · BBS/B/13470 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/E011640/1 · United Kingdom
External Links
PubMed source DOI: 10.1093/database/baw093 PMC Full Text View journal details
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